From owner-chemistry@ccl.net Wed May 29 08:17:01 2013 From: "Fedor Goumans goumans(~)scm.com" To: CCL Subject: CCL: Coordination / Solvation - Layer Message-Id: <-48747-130529045348-6849-UGHowgqKglTiwrZ6nR4SDg|*|server.ccl.net> X-Original-From: Fedor Goumans Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=windows-1252; format=flowed Date: Wed, 29 May 2013 10:52:45 +0200 MIME-Version: 1.0 Sent to CCL by: Fedor Goumans [goumans[]scm.com] Hi Joseph, It depends on what you want to 'simulate'. If you want to take into account the effect of the solvent layers on the properties of your molecule (e.g. solvation free energy, UV/VIS spectrum), you may look into 3D-RISM. Since all the statistical mechanics is dealt with in the integral equations for the solvent-solute interactions, this will circumvent the sampling problem you would have when you would run (AI)MD simulations. However, if your solvent layers somehow actively participate in a reaction coordinate, you may have to resort to advanced MD techniques like adaptive QM/MM where molecules may move between the QM and MM regions. Hope this helps, Best wishes, Fedor On 5/28/2013 9:31 PM, Joseph E Maxwell jaymax36|gmail.com wrote: > > Sent to CCL by: Joseph E Maxwell [jaymax36=gmail.com] > Hi List, > > Does anyone know if there are any programs available to simulate the > coordination layer(s) of say the first and second aqueous solvation > layer around a molecule. Say, a medium size organic molecule ~ 50 - > 190 Daltons, hydrophobic, apolar, polar would also be of particular > interest. > > Thankshttp://www.ccl.net/chemistry/sub_unsub.shtmlConferences: > http://server.ccl.net/chemistry/announcements/conferences/> > -- Dr. T. P. M. (Fedor) Goumans Business Developer Scientific Computing & Modelling NV (SCM) Vrije Universiteit, FEW, Theoretical Chemistry De Boelelaan 1083 1081 HV Amsterdam, The Netherlands T +31 20 598 7625 F +31 20 598 7629 E-mail: goumans~~scm.com http://www.scm.com From owner-chemistry@ccl.net Wed May 29 09:39:01 2013 From: "Herbert Fruchtl herbert.fruchtl(~)st-andrews.ac.uk" To: CCL Subject: CCL: CCP5 / ScotCHEM meeting 13/14 June 2013 in St Andrews Message-Id: <-48748-130529093649-4171-pYhTgfGoItD5b5LZiOwvhQ##server.ccl.net> X-Original-From: Herbert Fruchtl Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Wed, 29 May 2013 14:36:26 +0100 MIME-Version: 1.0 Sent to CCL by: Herbert Fruchtl [herbert.fruchtl(!)st-andrews.ac.uk] A half-day CCP5(*) workshop on "Modelling the Chemistry and Biochemistry of Condensed Phases" with a high-profile international all-female list of speakers, including a networking meeting with and for female scientists (but open to all) will be followed by the 7th ScotCHEM Computational Chemistry Symposium, where researchers from Scotland and beyond present their latest results in the field in form of contributed talks and a poster session. Program and registration (free) are available here: http://chemistry.st-andrews.ac.uk/staff/buehl/group/ScotChem2013/index.html Herbert (*) For non-Brits: The CCP's (Collaborative Computational Projects) are consortia of academics with focus on a certain field. CCP5 is "computer simulation of condensed phases". See http://www.ccp5.ac.uk/. -- Herbert Fruchtl Senior Scientific Computing Officer School of Chemistry, School of Mathematics and Statistics University of St Andrews -- The University of St Andrews is a charity registered in Scotland: No SC013532 From owner-chemistry@ccl.net Wed May 29 18:28:01 2013 From: "Ayyaz Mahmood ayyazcmc*gmail.com" To: CCL Subject: CCL: Running IRC calculations Message-Id: <-48749-130529182154-24301-zDlhMGIWwsZYukEW8qS/4Q*o*server.ccl.net> X-Original-From: "Ayyaz Mahmood" Date: Wed, 29 May 2013 18:21:53 -0400 Sent to CCL by: "Ayyaz Mahmood" [ayyazcmc-*-gmail.com] Hi everyone, While running IRC calculation, both forward and reverse calculation go to the same direction (i.e product) I tried running simple IRC without adding keyword, reverse or forward but the both ends of the curve gave the product. Anyone can please help me here, Thanking in anticipation.